19-4543904-C-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_032108.4(SEMA6B):āc.2364G>Cā(p.Pro788=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000474 in 1,202,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00027 ( 0 hom., cov: 32)
Exomes š: 0.000016 ( 0 hom. )
Consequence
SEMA6B
NM_032108.4 synonymous
NM_032108.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.555
Genes affected
SEMA6B (HGNC:10739): (semaphorin 6B) This gene encodes a member of the semaphorin family, a group of proteins characterized by the presence of a conserved semaphorin (sema) domain. Whereas some semaphorins are transmembrane proteins, others are secreted. Semaphorins play a major role in axon guidance. The protein encoded by this gene may be involved in both peripheral and central nervous system development. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 19-4543904-C-G is Benign according to our data. Variant chr19-4543904-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 792322.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
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Synonymous conserved (PhyloP=0.555 with no splicing effect.
BS2
?
High AC in GnomAd4 at 40 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA6B | NM_032108.4 | c.2364G>C | p.Pro788= | synonymous_variant | 17/17 | ENST00000586582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA6B | ENST00000586582.6 | c.2364G>C | p.Pro788= | synonymous_variant | 17/17 | 1 | NM_032108.4 | P1 | |
SEMA6B | ENST00000586965.1 | c.1851+513G>C | intron_variant | 1 | |||||
SEMA6B | ENST00000676793.1 | c.2364G>C | p.Pro788= | synonymous_variant | 17/17 | P1 | |||
SEMA6B | ENST00000677828.1 | c.*1626G>C | 3_prime_UTR_variant, NMD_transcript_variant | 17/17 |
Frequencies
GnomAD3 genomes ? AF: 0.000266 AC: 40AN: 150210Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000162 AC: 17AN: 1051910Hom.: 0 Cov.: 33 AF XY: 0.0000201 AC XY: 10AN XY: 496362
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GnomAD4 genome ? AF: 0.000266 AC: 40AN: 150314Hom.: 0 Cov.: 32 AF XY: 0.000286 AC XY: 21AN XY: 73422
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at